BioSequenceModify

BioSequenceModify[seq,"mod"]

gives the result of applying the modification "mod" to the sequence seq.

BioSequenceModify[seq,{"mod",params}]

specifies the parameters params for "mod".

BioSequenceModify[modspec]

represents an operator form of BioSequenceModify that can be applied to a biomolecular sequence.

Details

Bond modifications:

	{"AddBond",{i₁,i₂}}	add a higher-order bond between letters at i₁ and i₂
	{"AddBond",Bond[{i₁,i₂},"type"]}	add a bond of the given type between the given indices
	{"DeleteBond",{i₁,i₂}}	remove all higher-order bonds between the given indices
	{"DeleteBond",Bond[{i₁,i₂},"type"]}	remove the specified bond between the given indices

Circularity adjustment modifications:

	"MakeCircular"	convert a linear sequence into a circular sequence
	"MakeLinear"	convert a circular sequence into a linear sequence
	{"MakeLinear",i}	convert to a linear sequence, starting at the i position

Collection modifications:

	{"AddToCollection",{seq₁,seq₂,…}}	incorporate a list of sequences into a sequence collection
	"SplitDisconnectedCollection"	separate unbonded clusters into separate collections

Representation-only modifications:

	"InnermostBondRepresentation"	represent bonds at the innermost applicable sequence
	"OutermostBondRepresentation"	represent bonds at the outermost sequence
	"CanonicalRepresentation"	convert all sequences and bonds to a canonical form

Translation modifications:

	"DropIncompleteCodons"	drop incomplete codons from the end of DNA or RNA
	"DropToStartCodon"	drop letters from DNA or RNA until a start codon is found
	"DropFromStopLetter"	drop the letters from a peptide after a stop letter is found

Examples

open allclose all

Basic Examples (12)

Add a bond to a sequence:

Delete a bond from a sequence:

Represent all bonds at the innermost sequence, with all letters included:

Represent all bonds at the outermost sequence:

Canonicalize the representation of bonds and sequences into a sorted and reduced form:

Convert a linear sequence to a circular sequence:

Convert a circular sequence to a linear sequence:

Add a list of sequences into a sequence collection:

Separate the unbound components of a sequence collection into separate collections:

Drop letters at the end of a nucleotide sequence so only complete codons are present for translation:

Drop the letters up to a start codon in the default genetic translation table:

Drop terms after the stop letter in a peptide sequence:

Scope (23)

"AddBond" (4)

A bond type does not need to be specified to insert a bond. If one is not given, it will be inferred:

The type of the bond inferred may depend on the letters being linked:

Bonds can be added to hybrid strands:

Bonds can be added to sequence collections:

"AddToCollection" (3)

A single sequence can also be added to a collection:

A single motif or hybrid sequence will be modified into a collection:

If there are multiple sequence collections, they will be merged in the result:

"CanonicalRepresentation" (3)

If sequences are identical, canonicalization will use strand-level bonds for ordering:

If the sequences and strand-level bonds are identical, canonicalization will use sequence bonds for ordering:

In addition to sorting, single-strand collections are reduced to the strand and single motif hybrids are reduced to the motif:

"DeleteBond" (2)

Delete all higher-order bonds between the two indexes:

Deleting bonds always works on the outermost form, which is the form given by the "SequenceBondList" property:

"DropToStartCodon" (3)

Any genetic translation table entity can be used to specify start codons:

A specific codon or list of codons can be used as the start codon specification:

Modifications can be created in an operator form for later use:

Modifications with further specifications can also be used in operator form:

"InnermostBondRepresentation" (1)

Moving bonds inward can potentially bring them into the motif from several layers:

"MakeCircular" (2)

RNA sequences can be converted to circular RNA sequences:

Peptide sequences can be converted to circular peptide sequences:

"MakeLinear" (3)

Circular RNA sequences can be converted to linear RNA sequences:

Circular peptide sequences can be converted to linear peptide sequences:

Start the linear sequence from a specific position:

Relative bond positions are preserved when converting circular sequences to linear sequences:

"OutermostBondRepresentation" (1)

Moving bonds inward will bring them from inside any motif or strand to the outermost sequence structure:

"SplitDisconnectedCollection" (1)

Splitting connections will renumber bonds based on new collection memberships:

Applications (1)

A circular peptide:

Various peptides can be related to each other through a circular permutation:

Possible Issues (2)

A given modification may not apply to a particular type of sequence:

If a bond type cannot be inferred, an untyped bond is added:

Neat Examples (1)

Represent the protein preproinsulin as a BioSequence:

Remove the signal peptide sequence to make proinsulin:

Add the disulfide bonds and split the proinsulin sequence to make insulin:

Top

BioSequenceModify

Details

Examples

Basic Examples (12)